Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems

In biological processes, intrinsic noise, spatial heterogeneity and molecular crowding deeply affect the system dynamics. The classic stochastic methods lack of the necessary features needed for the description of these phenomena. Membrane systems are a suitable framework to embed these characteristics; in particular, the variants of tau-DPP and S tau-DPP allow the modelling and stochastic simulations of multi-volume biochemical systems, in which diffusion and size of volumes and chemicals are taken into account improving the description of these biological systems. In this paper we show, by means of two models of reaction-diffusion and crowded systems, the correctness and accuracy of our simulation methods.